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(-) Description

Title :  CRYSTAL STRUCTURE OF HELICOBACTER PYLORI UNDECAPRENYL PYROPHOSPHATE SYNTHASE COMPLEXED WITH PYROPHOSPHATE
 
Authors :  R. T. Guo, C. J. Kuo, C. L. Chen, T. P. Ko, P. H. Liang, A. H. -J. Wang
Date :  13 Jul 06  (Deposition) - 26 Jun 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Crystal Structure, Helicobacter Pylori, Cis Prenyltransferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. J. Kuo, R. T. Guo, I. L. Lu, H. G. Liu, S. Y. Wu, T. P. Ko, A. H. -J. Wang, P. H. Liang
Biochemical Characterization, Crystal Structure, And Inhibitors Of Helicobacter Pylori Undecaprenyl Pyrophosphate Synthase
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UNDECAPRENYL PYROPHOSPHATE SYNTHASE
    Chains: A, B
    EC Number: 2.5.1.31
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET32 XA/LIC
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 210

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1DPO1Ligand/IonDIPHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP B:13 , GLY B:14 , ASN B:15 , GLY B:16 , ARG B:17 , ARG B:26BINDING SITE FOR RESIDUE DPO B 426

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2DTN)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2DTN)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2DTN)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UPP_SYNTHASEPS01066 Undecaprenyl pyrophosphate synthase family signature.ISPT_HELPY176-193
 		  2A:176-193
B:176-193

(-) Exons   (0, 0)

(no "Exon" information available for 2DTN)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:214
 aligned with ISPT_HELPY | P55984 from UniProtKB/Swiss-Prot  Length:234

    Alignment length:224
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222    
           ISPT_HELPY     3 NTLKHLAIIMDGNGRWAKLKNKARAYGHKKGVKTLKDITIWCANHKLECLTLYAFSTENWKRPKSEVDFLMKMLKKYLKDERSTYLNNNIRFRAIGDLEGFSKELRDTILQLENDTRHFKDFTQVLALNYGSKNELSRAFKSLLESPPSHINLLESLENEISNRLDTHDLPEVDLLLRTGGEMRLSNFLLWQSSYAELFFTPILWPDFTPKDLENIISDFYKRV 226
               SCOP domains d2dtna_ A: automated matches                                                                                                                                                                                                     SCOP domains
               CATH domains 2dtnA00 A:3-226  [code=3.40.1180.10, no name defined]                                                                                                                                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee..hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...eeeee..----------hhhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhhhhhhhhh.......eeeee...hhhhhhhhhhhhhhhh.hhhhhhh..hhhhhhh...........eeee..................eeee...hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------UPP_SYNTHASE      --------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dtn A   3 STLKHLAIIMDGNGRWAKLKNKARAYGHKKGVKTLKDITIWCANHKLECLTLYAF----------EVDFLMKMLKKYLKDERSTYLDNNIRFRAIGDLEGFSKELRDTILQLENDTRHFKDFTQVLALNYGSKNELSRAFKSLLESPPSNISLLESLENEISNRLDTRNLPEVDLLLRTGGEMRLSNFLLWQSSYAELFFTPILWPDFTPKDLENIISDFYKRV 226
                                    12        22        32        42        52    |    -     |  72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222    
                                                                                 57         68                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:203
 aligned with ISPT_HELPY | P55984 from UniProtKB/Swiss-Prot  Length:234

    Alignment length:228
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223        
           ISPT_HELPY     4 TLKHLAIIMDGNGRWAKLKNKARAYGHKKGVKTLKDITIWCANHKLECLTLYAFSTENWKRPKSEVDFLMKMLKKYLKDERSTYLNNNIRFRAIGDLEGFSKELRDTILQLENDTRHFKDFTQVLALNYGSKNELSRAFKSLLESPPSHINLLESLENEISNRLDTHDLPEVDLLLRTGGEMRLSNFLLWQSSYAELFFTPILWPDFTPKDLENIISDFYKRVRKFGE 231
               SCOP domains d2dtnb_ B: automated matches                                                                                                                                                                                                         SCOP domains
               CATH domains 2dtnB00 B:4-231  [code=3.40.1180.10, no name defined]                                                                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...eeeeee----------------hhhhhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhhhhhhhhhhh......eeeeeee..hhhhhhhhhhhhhhhh.---------hhhhhhh...........eeee..................eeee...hhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------UPP_SYNTHASE      -------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2dtn B   4 TLKHLAIIMDGNGRWAKLKNKARAYGHKKGVKTLKDITIWCANHKLECLTLYA----------------MKMLKKYLKDERSTYLDNNIRFRAIGDLEGFSKELRDTILQLENDTRHFKDFTQVLALNYGSKNELSRAFKSLLESP---------LENEISNRLDTRNLPEVDLLLRTGGEMRLSNFLLWQSSYAELFFTPILWPDFTPKDLENIISDFYKRVRKFGE 231
                                    13        23        33        43        53  |      -        73        83        93       103       113       123       133       143     |   -     | 163       173       183       193       203       213       223        
                                                                               56               73                                                                         149       159
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DTN)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (ISPT_HELPY | P55984)
molecular function
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004659    prenyltransferase activity    Catalysis of the transfer of a prenyl group from one compound (donor) to another (acceptor).
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016765    transferase activity, transferring alkyl or aryl (other than methyl) groups    Catalysis of the transfer of an alkyl or aryl (but not methyl) group from one compound (donor) to another (acceptor).

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        ISPT_HELPY | P55984: 2d2r

(-) Related Entries Specified in the PDB File

2d2r THE SAME PROTEIN (APO FORM)